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What is emitting these error messages, OmniFocus, or the Mac? It sounds to me like your database is getting synced by MobileMe's iDisk sync as well as by OmniFocus. Running the three OmniFocus apps together should not cause any trouble like this I do it all the time, dozens of syncs a day, often making changes on all of the devices between syncs.

If you aren't using the Mail->OmniFocus processing, why not just quit the Mac app, if you think that is the source of the trouble?